affinegap

library1.12pypypi✓ verified 84d ago

A Cython implementation of the affine gap string distance for measuring string similarity with affine gap penalties. Current version 1.12, stable but rarely updated.

ai-ml

pip install affinegap

github ↗package ↗

INSTALL

IMPORT

SIG · AFFINEGAP

affinegap

ai-mlpythonv1.12

Install

1.6s avg

Import

—

Disk

18MB

Pass rate

4/ 10

Env Coverage4 / 10

glibc

3.9–3.13

musl

3.9–3.13

Install & Compatibility

Where this runs

tested against v1.12 · pip install

no network on importno background threads

Install × environment matrix

Each cell = how many times install + import succeeded across repeated harness runs. Partial = flaky.
glibc = Debian/Ubuntu slim · musl = Alpine Linux

musl

glibc

py 3.10

✓ —

✓ 1.5s

py 3.11

✕ build_error

py 3.12

✕ build_error

py 3.13

✕ build_error

py 3.9

✓ —

✓ 1.7s

18MB installed

● package 18MB

Code

Verified usage

Verified import paths — ran on the pinned version, not inferred.

affinegap

✓ import affinegap

✗ from affinegap import affinegap

affinegap is the module itself, not a function named affinegap; the main function is accessed as affinegap.affineGapDistance

Basic usage: compute affine gap string distance. The function returns an integer distance or similarity score depending on penalties.

import affinegap # Compute affine gap distance between two strings dist = affinegap.affineGapDistance("string1", "string2") print(dist) # With custom gap penalties dist = affinegap.affineGapDistance("hello", "hallo", match_weight=0, mismatch_weight=1, gap_weight=1, spatial_gap_weight=1) print(dist)

Debug

Known issues

gotchaThe function is named `affineGapDistance` (capital G) not `affinegap`. Many users mistakenly try `affinegap.distance()`.

fix

Use `affinegap.affineGapDistance(s1, s2)`

affects: all

gotchaDefault behavior: by default, match_weight=0, mismatch_weight=1, gap_weight=1, spatial_gap_weight=1. This means identical strings get distance 0, but a single mismatch or gap adds 1. This may not be what you expect for 'similarity'.

fix

Adjust parameters: e.g., match_weight=-1, mismatch_weight=1, gap_weight=-1 for similarity-like scores.

affects: all

gotchaAffine gap distance is not symmetric? Actually it is symmetric, but careful: the function expects two strings; if you pass integer or None, it may throw TypeError.

fix

Ensure both arguments are strings.

affects: all

Errors

Common errors & fixes

ImportError: cannot import name 'affinegap'

Trying to do `from affinegap import affinegap` instead of `import affinegap`.

fix

Replace with `import affinegap` and use `affinegap.affineGapDistance`.

AttributeError: module 'affinegap' has no attribute 'affinegap'

Same as above - the module does not contain a function named affinegap.

fix

Use `affinegap.affineGapDistance`.

TypeError: expected string or Unicode object

Passing a non-string (e.g., integer) to affineGapDistance.

fix

Convert arguments to strings: `affinegap.affineGapDistance(str(a), str(b))`

Upgrade

Version history

1.12latest on PyPI · released Jan 1, 2022

Audit

Dependencies

No dependency data recorded yet.

Agent activity

61 hits · last 30 days

node

OpenAI (training)

Resources

githubhttps://github.com/datamade/affinegap ↗

packagehttps://pypi.org/project/affinegap/ ↗